Sadly, no. Parmed only shows 8 bonds where two are missing.
> printBonds :FE1
Atom 1 Atom 2 R eq Frc Cnst
22 C9 ( Z1) 24 FE ( M1) 2.0449 87.0000
20 C8 ( Y4) 24 FE ( M1) 2.0519 84.0000
18 C7 ( Y3) 24 FE ( M1) 2.0523 83.5000
16 C6 ( Y2) 24 FE ( M1) 2.0534 84.9000
15 C5 ( Y1) 24 FE ( M1) 2.0480 75.7000
24 FE ( M1) 25 C10 ( Y6) 2.0521 85.3000
24 FE ( M1) 27 C11 ( Y7) 2.0538 85.1000
24 FE ( M1) 29 C12 ( Y8) 2.0539 84.7000
Best regards
// Gustaf
> On 13 Aug 2021, at 11:56, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> I realised that the “duplicate records” were likely the ones in the TEST_tleap.in file where there are repeating bonds defined to iron:
>
> bond mol.1.C5 mol.2.FE
> bond mol.1.C5 mol.2.FE
> bond mol.1.C6 mol.2.FE
> bond mol.1.C6 mol.2.FE
> bond mol.1.C7 mol.2.FE
> bond mol.1.C7 mol.2.FE
> bond mol.1.C8 mol.2.FE
> bond mol.1.C8 mol.2.FE
> bond mol.1.C9 mol.2.FE
> bond mol.1.C9 mol.2.FE
> bond mol.1.C9 mol.2.FE
> bond mol.1.C9 mol.2.FE
> bond mol.2.FE mol.3.C10
> bond mol.2.FE mol.3.C10
> bond mol.2.FE mol.3.C11
> bond mol.2.FE mol.3.C11
> bond mol.2.FE mol.3.C12
> bond mol.2.FE mol.3.C12
> bond mol.2.FE mol.3.C13
> bond mol.2.FE mol.3.C13
>
> So I kept the “gaff2” source in and removed all the duplicate entries:
>
> bond mol.1.C5 mol.2.FE
> bond mol.1.C6 mol.2.FE
> bond mol.1.C7 mol.2.FE
> bond mol.1.C8 mol.2.FE
> bond mol.1.C9 mol.2.FE
> bond mol.2.FE mol.3.C10
> bond mol.2.FE mol.3.C11
> bond mol.2.FE mol.3.C12
> bond mol.2.FE mol.3.C13
>
> This seems to have worked though in the mcpb.in file I defined 10 bonds:
>
> add_bonded_pairs 24-15 24-16 24-18 24-20 24-22 24-25 24-27 24-29 24-31 24-22
>
> and I cannot help but notice that there are only 9 bonds added here. In VDM the “FE1.FE 3.C13” nondescripts is not visualised, I am only seeing eight. I manually added the missing " bond mol.2.FE mol.3.C14” to the input
>
> bond mol.1.C5 mol.2.FE
> bond mol.1.C6 mol.2.FE
> bond mol.1.C7 mol.2.FE
> bond mol.1.C8 mol.2.FE
> bond mol.1.C9 mol.2.FE
> bond mol.2.FE mol.3.C10
> bond mol.2.FE mol.3.C11
> bond mol.2.FE mol.3.C12
> bond mol.2.FE mol.3.C13
> bond mol.2.FE mol.3.C14
>
> By removing duplicates I was also able to drop the "set mol.2.FE pert true” part, this is no longer needed.
>
> cpptraj -p TEST_solv.prmtop
>
> Now produces no errors. However, VMD still does not visualise all 10 bonds to FE, only 8. I have experienced before other visualisation issue before and my hope is that this is only a visualisation problem?
>
> Best regards
> // Gustaf
>
>> On 13 Aug 2021, at 11:17, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> After some work I managed to get through steps 2-4 of MCPB though now I am stuck at the tleap step.
>>
>> I have all the files that are indicated and these generally look to be OK. I ran tleap with the generated input file and received repeats of to general errors:
>>
>> Bond: Maximum coordination exceeded on .R<FE1 2>.A<FE 1>
>> -- setting atoms pert=true overrides default limits
>>
>> and
>>
>> amber20/bin/teLeap: Error!
>> For atom (.R<LG1 1>.A<C1 1>) could not find vdW (or other) parameters for type (c2)
>>
>> I figured the latter one is because i only have non-amino acid residues parameterised using gaff2 with antechamber and parmchk2. So I added a line sourcing gaff2 in the TEST_tleap.in file producing an additional error:
>>
>> !FATAL ERROR----------------------------------------
>> !FATAL: In file [/Users/guolaa/SOFTWARE/amber20_src/AmberTools/src/leap/src/leap/unitio.c], line 1808
>> !FATAL: Message: 1-4: cannot add bond 20 24
>> This may be caused by duplicate bond specifications;
>> for example, explicit bond commands in addition to PDB conect records.
>> !
>> !ABORTING.
>>
>> There are no connect records in the TEST_mcbppy.pdb file generated and while this error message obviously refers to the same issue, is a lot less informative then the repeating instances of the error above, carbon bonds to ion. I really need a win here to end the week on a good note :)
>>
>> 1) Can I assume that I am correct that “source.leaprc.gaff2” needs to be added to the TEST_tleap.in file?
>>
>> 2) Is the " !FATAL ERROR” likely caused by the "Bond: Maximum coordination exceeded” problem?
>>
>> I am trying to figure out how to use “set” to include the "pert=true” as suggested though have not managed to figure it out just get.
>>
>> As usual I am attaching my files in hope of some helt identifying and hopefully solving this problem.
>>
>> Best regards
>> // Gustaf
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> <FE1.mol2><LG1.mol2><LRG.frcmod><SL1.mol2><SML.frcmod><TEST_mcpbpy.frcmod><TEST_mcpbpy.pdb><TEST_tleap.in>_______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 13 2021 - 03:30:02 PDT
